[gmx-users] gromacs on GPU

[James Starlight]

Roland,

indeed the error was that I'have compilate mdrun-openmm which is not
the native gpu.

now I've made mdrun via

cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0

and obtain workable gromacs.

My test system consist of calmodulin (charmm27) solvated in tip3p
water. total size of the system: 67752 atoms.
I have set below values on the mdp file as grompp told me

nstlist = 20
cutoff-scheme = Verlet   ; !not quite sure whai is this!
vdwtype         = cut-off


 Now on the mdrun output I have

Using 1 MPI thread
Using 4 OpenMP threads

1 GPU detected:
  #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC:  no, stat: compatible

1 GPU auto-selected to be used for this run: #0

does it mean that all 4 cores of my CPU + gpu are used at same time ?
is there any other ways to increase performance ? ( e.g I'm not quite
sure if open_mpi is used with that build because during compilation
cmake asked me only about fftw3 libs).

Is there any ways to monitor total performance ( e.g separate cpu and
gpu usage ) ?


Thanks for suggestions,

James

2013/1/9 Roland Schulz <roland at utk.edu>:
> On Wed, Jan 9, 2013 at 3:17 AM, James Starlight <jmsstarlight at gmail.com>wrote:
>
>> As I understood that gromacs version already has included openMM so
>> the installation of the external openMM sources is not needed, isnt it
>> ?
>>
>
> No the new build in GPU implementation and openMM are two different things.
> The Gromacs-OpenMM interface isn't actively maintained and thus not
> recommended.
>
>
>> also I wounder to know what exactly CUDA version is needed ? For
>> example I've tried lattest cuda-5.0 but with that version i've obtain
>> error from mdrun-openmm that platform cuda was not detected (gromacs
>> was compilated without any errors).
>>
> with the natived gpu implementation (GMX_GPU) cuda 5.0 works fine.
>
>
>> by the way is it possible to compilate gromacs-4.6 agains other
>> platgorm ( e.g openCL) ? I have no problems with the compatibility of
>> the openCL and openMM.
>>
> GMX_GPU doesn't support openCL.
>
> Roland
>
>
>>
>> James
>>
>> 2013/1/9 Szilárd Páll <szilard.pall at cbr.su.se>:
>> > On Tue, Jan 8, 2013 at 3:22 PM, James Starlight <jmsstarlight at gmail.com
>> >wrote:
>> >
>> >> So could someone provide me more about gpu-accelerated MD implemented
>> >> in the 4.6 gromacs ? Does it require openMM (what version is supported
>> >>
>> >
>> > FYI, if nobody can, trust G:
>> > http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
>> > http://lmgtfy.com/?q=gromacs+4.6+installation+instructions
>> >
>> > The wiki and mailing list contains quite extensive information (indexed
>> by
>> > G).
>> >
>> > Otherwise, release notes (not final):
>> > http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
>> >
>> > Install guide is at the expected location:
>> > http://www.gromacs.org/Documentation/Installation_Instructions
>> >
>> > Cheers,
>> > --
>> > Szilárd
>> >
>> >
>> >> for that gromacs release ?) installed? By the way at present time I
>> >> force with the problem of compilation 4.1.1 openMM (i need to compile
>> >> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
>> >> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
>> >>
>> >>
>> >> James
>> >>
>> >> 2013/1/7 James Starlight <jmsstarlight at gmail.com>:
>> >> > Hi Szilárd!
>> >> >
>> >> > As I understood you correctly gromacs-4.6 have specific algorithm
>> >> > (independent on openMM?) for gpu-based calculations havent ? If it
>> >> > true how I should compilate such new gpu-based gromacs? In the
>> >> > gromacs-4.6-beta-3 folder I've found instructuon for the standart
>> >> > installation via cmake
>> >> >
>> >> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
>> >> >
>> >> >
>> >> > James
>> >> >
>> >> > 2013/1/7 Szilárd Páll <szilard.pall at cbr.su.se>:
>> >> >> Szilárd
>> >> --
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